Ok. I've investigated this - I will add a better fix to the next version, but for now I suggest setting it in the tk2dCamera.Start function, or your own script (you don't need tk2dCamera for a perspective camera anyway).
The older behaviour in 2.0 was leaking memory - the transparencysortmode function shouldn't be called every frame as it allocates memory. Turns out that value isn't saved in Unity, which makes the current fix not work as it should.